[gmx-users] dynamic cross correlation map (DCCM)

[Justin A. Lemkul]

leila karami wrote:
> Hi
>  
> I want to obtain dynamic cross correlation map (DCCM). I used following 
> command for obtaining covariance matrix.
>  
> g_covar -f traj.xtc -s topol.tpr -o eigenval.xvg -v eigenvec.trr -l 
> covar.log -xpm covar.xpm.
>  
> my system consists protein of 70 aminoacids. I want survey correlated 
> and anti-correlated motion between residues.
>  
> Is my manner true? If so, which of output files in above give me dynamic 
> cross correlation map (DCCM)? otherwise, please guide me.
> 

No one has ever been able to explain to me the difference between DCCM and PCA, 
so I'd say you're correct at least in obtaining the covariance matrix, which 
will give you information about correlated and anticorrelated motion.  "DCCM" 
seems to be a popular term with the AMBER crowd, but I don't know that their 
manual even gives the equations used for such an analysis to potentially 
differentiate it from PCA.  I believe there are some tips in their mail 
reflector, however.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================